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2013 IEEE 9th International Conference on e-Science最新文献

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An Autonomous Security Storage Solution for Data-Intensive Cooperative Cloud Computing 面向数据密集型协同云计算的自主安全存储解决方案
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.31
Wenchao Jiang, Zhiming Zhao, C. D. Laat
In order to reduce untrustworthy between cloud users and the underlying cloud storage platform, a novel cloud security storage solution is proposed based on autonomous data storage, management, and access control. The roles of users are re-evaluated, and the knowledge provided by the users is incorporated into the cloud storage model. Both the superiority of the public cloud in large scale data storage and the advantages of the private cloud in privacy preserving can be obtained. The main advantages of our approach include avoiding the superposition of complex security policies and overcoming the mistrust between the users and the platform. Furthermore, our security storage service can be easily integrated into the cooperative cloud computing environment. A prototype system is developed, and a use case is also presented.
为了减少云用户与底层云存储平台之间的不信任感,提出了一种基于数据自主存储、管理和访问控制的云安全存储解决方案。重新评估用户的角色,将用户提供的知识整合到云存储模型中。既可以获得公有云在大规模数据存储方面的优势,又可以获得私有云在隐私保护方面的优势。该方法的主要优点包括避免了复杂安全策略的叠加,克服了用户和平台之间的不信任。此外,我们的安全存储服务可以轻松集成到协作云计算环境中。开发了一个原型系统,并给出了一个用例。
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引用次数: 4
Using Link Prediction to Estimate the Collaborative Influence of Researchers 利用链接预测估计研究人员的协作影响
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.32
Evelyn Perez Cervantes, J. Mena-Chalco, Maria Cristina Ferreira de Oliveira, R. M. C. Junior
The influence of a particular individual in a scientific collaboration network could be measured in several ways. Estimating influence commonly requires calculating computationally costly global measures, which may be impractical on networks with hundreds of thousands of vertices. In this paper, we introduce new local measures to estimate the collaborative influence of individual researchers in a collaboration network. Our approach is based on the link prediction technique, and its underlying rationale is to assess how the presence/absence of a researcher affects the link prediction outcome in the network as a whole. It is natural to assume that the absence of a researcher with strong influence in the network will cause negative impact in the correct link prediction. Scientists are represented as vertices in the collaboration graph, and a vertex removal and corresponding link prediction process are performed iteratively for all vertices, each vertex being handled independently. The SVM supervised learning model has been adopted as link predictor. The proposed approach has been tested on real collaboration networks relative to multiple time periods, processing the networks in order to assign more relevance to recent than to older collaborations. The experimental tests suggest that our measure of impact on link prediction has high negative correlation with standard vertex importance measures such as between ness and closeness centrality.
一个特定个体在科学合作网络中的影响力可以用几种方法来衡量。估计影响通常需要计算计算成本很高的全局度量,这在具有数十万个顶点的网络上可能是不切实际的。在本文中,我们引入了新的局部度量来估计协作网络中单个研究人员的协作影响。我们的方法基于链接预测技术,其基本原理是评估研究人员的存在/不存在如何影响整个网络中的链接预测结果。人们很自然地认为,如果没有一个在网络中具有较强影响力的研究者,会对正确的链路预测产生负面影响。将科学家表示为协作图中的顶点,并对所有顶点迭代执行顶点移除和相应的链接预测过程,每个顶点独立处理。采用支持向量机监督学习模型作为链路预测器。所提出的方法已经在多个时间段的真实协作网络上进行了测试,对网络进行处理,以便为最近的协作分配更多的相关性,而不是旧的协作。实验测试表明,我们对链接预测的影响度量与标准顶点重要性度量(如关联度和密切度中心性)具有高度负相关。
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引用次数: 18
A Robust and Scalable Solution for Interpolative Multidimensional Scaling with Weighting 加权插值多维尺度的鲁棒可伸缩解
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.30
Yang Ruan, G. Fox
Advances in modern bio-sequencing techniques have led to a proliferation of raw genomic data that enables an unprecedented opportunity for data mining. To analyze such large volume and high-dimensional scientific data, many high performance dimension reduction and clustering algorithms have been developed. Among the known algorithms, we use Multidimensional Scaling (MDS) to reduce the dimension of original data and Pair wise Clustering, and to classify the data. We have shown that interpolative MDS, which is an online technique for real-time streaming in Big Data, can be applied to get better performance on massive data. However, SMACOF MDS approach is only directly applicable to cases where all pair wise distances are used and where weight is one for each term. In this paper, we proposed a robust and scalable MDS and interpolation algorithm using Deterministic Annealing technique, to solve problems with either missing distances or a non-trivial weight function. We compared our method to three state-of-art techniques. By experimenting on three common types of bioinformatics dataset, the results illustrate that the precision of our algorithms are better than other algorithms, and the weighted solutions has a lower computational time cost as well.
现代生物测序技术的进步导致了原始基因组数据的激增,这为数据挖掘提供了前所未有的机会。为了分析如此大容量、高维的科学数据,人们开发了许多高性能的降维和聚类算法。在已知的算法中,我们使用多维尺度(MDS)对原始数据进行降维,并使用成对聚类对数据进行分类。我们已经证明,插值MDS是一种用于大数据实时流的在线技术,可以在海量数据上获得更好的性能。然而,SMACOF MDS方法仅直接适用于使用所有成对距离并且每个项的权重为1的情况。在本文中,我们提出了一种鲁棒且可扩展的MDS和插值算法,该算法使用确定性退火技术来解决缺失距离或非平凡权函数的问题。我们将自己的方法与三种最先进的技术进行了比较。通过对三种常见的生物信息学数据集的实验,结果表明,我们的算法的精度优于其他算法,并且加权解具有更低的计算时间。
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引用次数: 18
Plant Species Identification with Phenological Visual Rhythms 植物物候视觉节律的物种识别
Pub Date : 2013-10-22 DOI: 10.1109/ESCIENCE.2013.43
J. Almeida, J. A. D. Santos, Bruna Alberton, L. Morellato, R. Torres
Plant phenology studies recurrent plant life cycles events and is a key component of climate change research. To increase accuracy of observations, new technologies have been applied for phenological observation, and one of the most successful are digital cameras, used as multi-channel imaging sensors to estimate color changes that are related to phenological events. We monitored leaf-changing patterns of a cerrado-savanna vegetation by taken daily digital images. We extract individual plant color information and correlated with leaf phenological changes. To do so, time series associated with plant species were obtained, raising the need of using appropriate tools for mining patterns of interest. In this paper, we present a novel approach for representing phenological patterns of plant species derived from digital images. The proposed method is based on encoding time series as a visual rhythm, which is characterized by image description algorithms. A comparative analysis of different descriptors is conducted and discussed. Experimental results show that our approach presents high accuracy on identifying plant species.
植物物候学研究植物生命周期的周期性事件,是气候变化研究的重要组成部分。为了提高物候观测的准确性,新技术已被应用于物候观测,其中最成功的是数码相机,它被用作多通道成像传感器来估计与物候事件相关的颜色变化。我们通过每天拍摄数字图像来监测塞拉多稀树草原植被的叶子变化模式。提取植物单株颜色信息,并与叶片物候变化进行关联。为此,获得了与植物物种有关的时间序列,因此需要使用适当的工具来挖掘感兴趣的模式。在本文中,我们提出了一种新的方法来表示来自数字图像的植物物种物候模式。该方法基于将时间序列编码为视觉节奏,并通过图像描述算法对其进行表征。对不同的描述符进行了比较分析和讨论。实验结果表明,该方法对植物物种的识别具有较高的准确性。
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引用次数: 16
Accelerating Astronomical Image Subtraction on Heterogeneous Processors 在异构处理器上加速天文图像减法
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.23
Yan Zhao, Qiong Luo, Senhong Wang, Chao Wu
Image subtraction is an effective method used in astronomy to search transient objects or identify objects that have time-varying brightness. The state-of-the-art astronomical image subtraction methods work by taking two aligned images of the same observation area, calculating a space-varying convolution kernel for the two images, and finally obtaining the difference image using the convolution kernel. With the need for fast image subtraction in astronomy projects, we study the parallelization of HOTPANTS, a popular astronomical image subtraction package by Andrew Becker, on multicore CPUs and GPUs. Specifically, we identify the components in HOTPANTS that are data parallel and parallelize these components on the GPU and multicore CPU. We divide the work between the CPU and the GPU to minimize the overall time. In the GPU-based components, we investigate the suitable setup of the GPU thread structure for the computation, and optimize data access on the GPU memory hierarchy. Consequently, P-HOTPANTS (our parallel zed HOTPANTS), achieves a 4-times speedup over the original HOTPANTS running on a desktop with an Intel i7 CPU and an NVIDIA GTX580 GPU.
图像减法是天文学中搜索瞬变物体或识别具有时变亮度的物体的有效方法。目前最先进的天文图像减法方法是取同一观测区域的两幅对齐图像,计算两幅图像的空间变化卷积核,最后利用卷积核得到差分图像。针对天文项目中快速图像减法的需求,研究了由Andrew Becker设计的热门天文图像减法包HOTPANTS在多核cpu和gpu上的并行化。具体来说,我们在HOTPANTS中识别数据并行的组件,并在GPU和多核CPU上并行化这些组件。我们在CPU和GPU之间划分工作,以最大限度地减少总时间。在基于GPU的组件中,我们研究了适合计算的GPU线程结构的设置,并优化了GPU内存层次上的数据访问。因此,P-HOTPANTS(我们的并行HOTPANTS),实现了4倍的加速比原来的HOTPANTS运行在台式机与英特尔i7 CPU和NVIDIA GTX580 GPU。
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引用次数: 3
Automatic Outlier Detection for Genome Assembly Quality Assessment 基因组装配质量评估的自动异常值检测
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.49
T. Samak, R. Egan, Brian Bushnell, D. Gunter, A. Copeland, Zhong Wang
In this work we describe a method to automatically detect errors in de novo assembled genomes. The method extends a Bayesian assembly quality evaluation framework, ALE, which computes the likelihood of an assembly given a set of unassembled data. Starting from ALE output, this method applies outlier detection algorithms to identify the precise locations of assembly errors. We show results from a microbial genome with manually curated assembly errors. Our method detects all deletions, 82.3% of insertions, and 88.8% of single base substitutions. It was also able to detect an inversion error that spans more than 400 bases.
在这项工作中,我们描述了一种自动检测从头组装基因组错误的方法。该方法扩展了贝叶斯装配质量评估框架ALE,该框架计算给定一组未装配数据的装配的可能性。该方法从ALE输出出发,应用离群点检测算法识别装配误差的精确位置。我们展示的结果来自一个微生物基因组与人工策划组装错误。我们的方法检测到所有的缺失,82.3%的插入和88.8%的单碱基替换。它还能够检测到跨越400多个碱基的反演错误。
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引用次数: 1
Benchmarking Gender Differences in Volunteer Computing Projects 志愿者计算项目中的性别差异基准
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.29
Trilce Estrada, K. Pusecker, Manuel R. Torres, J. Cohoon, M. Taufer
Volunteer Computing (VC) uses the computational resources of volunteers with Internet-connected personal computers to address fundamental problems in science. Docking Home (D@H) is a VC project targeting drug discovery through high throughput docking simulations i.e., by docking small molecules (ligands) into target proteins associated to diseases. Currently there are more than 27,000 volunteers (and 70,000 computers) worldwide supporting D@H. Similar to national trends in STEM fields, in general, the huge majority of volunteers engaged in VC projects, and in D@H in particular, are Caucasian males. This paper aims to characterize the current VC community supporting D@H and uses the information to define strategies that can help attract and retain female and ethnic minority volunteers.
志愿计算(VC)利用志愿者的计算资源和连接互联网的个人计算机来解决科学中的基本问题。对接家园(D@H)是一个VC项目,通过高通量对接模拟,即通过将小分子(配体)对接到与疾病相关的靶蛋白中,靶向药物发现。目前,全球有超过27,000名志愿者(和70,000台计算机)支持D@H。与STEM领域的全国趋势类似,总体而言,从事风险投资项目的绝大多数志愿者,特别是D@H,都是白人男性。本文旨在描述目前支持D@H的VC社区的特征,并使用这些信息来定义有助于吸引和留住女性和少数民族志愿者的策略。
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引用次数: 9
Accelerating In-memory Cross Match of Astronomical Catalogs 加速天文表在内存中的交叉匹配
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.9
Senhong Wang, Yan Zhao, Qiong Luo, Chao Wu, Yang Xv
New astronomy projects generate observation images continuously and these images are converted into tabular catalogs online. Furthermore, each such new table, called a sample table, is compared against a reference table on the same patch of sky to annotate the stars that match those in the reference and to identify transient objects that have no matches. This cross match must be done within a few seconds to enable timely issuance of alerts as well as shipping of the data products off the pipeline. To perform the online cross match of tables on celestial objects, we propose two parallel algorithms, zone Match and grid Match, both of which divide up celestial objects by their locations in the spherical coordinate system. Specifically, zone Match divides the observation area by the declination coordinate of the celestial sphere whereas grid Match utilizes a two-dimensional grid on the declination and the right ascension. With the reference table indexed by zones or grid, we match the stars in the sample table through parallel index probes on the reference. We implemented these algorithms on a multicore CPU as well as a desktop GPU, and evaluated their performance on both synthetic data and real world astronomical data. Our results show that grid Match is faster than zone Match at the cost of memory space and that parallelization achieves speedups of orders of magnitude.
新的天文项目不断产生观测图像,这些图像被转换成在线表格目录。此外,每一个这样的新表(称为样本表)都要与同一块天空上的参考表进行比较,以注释与参考表中匹配的恒星,并识别没有匹配的瞬变物体。这种交叉匹配必须在几秒钟内完成,以便及时发出警报,并将数据产品从管道中传送出去。为了实现天体表的在线交叉匹配,我们提出了两种并行算法:区域匹配和网格匹配,这两种算法都是根据天体在球坐标系中的位置来划分天体。具体来说,区域匹配是用天球赤纬坐标来划分观测区域,而网格匹配是在赤纬和赤经上使用二维网格。对于以区域或网格为索引的参考表,我们通过对参考进行并行索引探测来匹配样本表中的星号。我们在多核CPU和桌面GPU上实现了这些算法,并在合成数据和真实世界的天文数据上评估了它们的性能。我们的结果表明,网格匹配比区域匹配更快,代价是内存空间,并行化实现了数量级的速度提升。
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引用次数: 7
Magic View: An Optimized Ultra-Large Scientific Image Viewer for SAGE Tiled-Display Environment 魔术视图:一个优化的超大科学图像查看器SAGE平铺显示环境
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.16
Yihua Lou, Haikuo Zhang, Wenjun Wu, Zhenghui Hu
Massive amount scientific data often need to be visualized in ultra-large images for scientific discovery. Although ultra-high resolution tiled-display environments have been widely used, there still lacks of proper image viewers that can display ultra-large images with billions of pixels in tiled-display environments. To address the problem, we propose Magic View, an optimized ultra-large scientific image viewer for SAGE tiled-display environment. It can achieve real-time interactive performance in viewing images with billions of pixels. Our experiments show that the performance of Magic View are at lease 8x better than Juxta View, another ultra-large image viewer for SAGE.
为了科学发现,往往需要将海量的科学数据可视化为超大图像。虽然超高分辨率的平铺显示环境已经得到了广泛的应用,但目前还缺乏合适的图像观看器,可以在平铺显示环境中显示数十亿像素的超大图像。为了解决这个问题,我们提出了Magic View,这是一个针对SAGE平铺显示环境优化的超大科学图像查看器。在观看数十亿像素的图像时,可以实现实时交互性能。我们的实验表明,Magic View的性能至少比SAGE的另一个超大图像查看器& & & View好8倍。
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引用次数: 1
Malleable Access Rights to Establish and Enable Scientific Collaboration 建立和实现科学合作的可延展性访问权
Pub Date : 2013-10-22 DOI: 10.1109/eScience.2013.26
Ferry Hendrikx, K. Bubendorfer
Collaborative systems require access control to prevent unauthorised access and change. Access control has a number of issues, including administration and maintenance overheads. In this paper we argue that it is time to reconsider how access controls work, particularly with scientific and data related domains, and to this end we propose a new paradigm based on a user's demographics and behaviour, rather than simply their identity. In essence, it is both who you are and what you do that is important. We introduce Graft, our Generalised Recommendation Architecture that allows us to support a range of different recommendation models, and provide case studies to illustrate the usefulness of our architecture.
协作系统需要访问控制以防止未经授权的访问和更改。访问控制有许多问题,包括管理和维护开销。在本文中,我们认为是时候重新考虑访问控制的工作方式了,特别是在科学和数据相关领域,为此,我们提出了一个基于用户人口统计和行为的新范式,而不仅仅是他们的身份。从本质上讲,重要的是你是谁和你做了什么。我们介绍了Graft,我们的通用推荐体系结构,它允许我们支持一系列不同的推荐模型,并提供案例研究来说明我们体系结构的有用性。
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引用次数: 5
期刊
2013 IEEE 9th International Conference on e-Science
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